Python rendering animation saves frame twice
So if anyone stumbles over this: I did find out what caused it

A bit unintuitively, Blender automatically saves animation but not single frames. I assumed that after I removed the default composite node (after activation nodes) in the Composition View, Blender would not save anything out of my designated output nodes. But well, it still does (but again, only when you render animations).

Edit (27-03-2020): To make it a bit clearer, the problem is that while you can choose not to save the output when rendering frames, Blender WILL saved rendered animations regardless of your dedicated output nodes. The option not to save this animation output (in addition to your output nodes) seems to be missing. 

There also doesn't seem an obvious way of preventing Blender from doing so which is quite annoying.